runSeuratJackStraw Compute jackstraw plot and store the computations in the input sce object

runSeuratJackStraw Compute jackstraw plot and store the computations in the input sce object

runSeuratJackStraw(
  inSCE,
  useAssay,
  dims = NULL,
  numReplicate = 100,
  propFreq = 0.025,
  externalReduction = NULL
)

Arguments

inSCE

(sce) object on which to compute and store jackstraw plot

useAssay

Specify name of the assay to use for scaling. Assay name provided against this parameter is scaled by the function and used for the computation of JackStraw scores along with the reduced dimensions specified by the dims parameter.

dims

Number of components to test in Jackstraw. If NULL, then all components are used. Default NULL.

numReplicate

Numeric value indicating the number of replicate samplings to perform. Default value is 100.

propFreq

Numeric value indicating the proportion of data to randomly permute for each replicate. Default value is 0.025.

externalReduction

Pass DimReduc object if PCA/ICA computed through other libraries. Default NULL.

Value

Updated SingleCellExperiment object with jackstraw computations stored in it

Examples

data(scExample, package = "singleCellTK")
if (FALSE) {
sce <- runSeuratNormalizeData(sce, useAssay = "counts")
sce <- runSeuratFindHVG(sce, useAssay = "counts")
sce <- runSeuratScaleData(sce, useAssay = "counts")
sce <- runSeuratPCA(sce, useAssay = "counts")
sce <- runSeuratJackStraw(sce, useAssay = "counts")
}